Tu, 25.8.2026 | Original article from: Thermo Fisher Scientific / Bashar Amer PhD
SQUAD metabolomics combines targeted quantitation and untargeted discovery in a single Orbitrap MS experiment, delivering confident quantitative results alongside broad metabolite profiling.One Injection, Two Answers: Introducing Squad Metabolomics on Orbitrap Mass Spectrometers
Thermo Fisher Scientific: One Injection, Two Answers: Introducing Squad Metabolomics on Orbitrap Mass Spectrometers
Metabolomics researchers are often forced to choose between two powerful but different approaches. Untargeted metabolomics is great for discovery: it surveys as many metabolites as possible to reveal biology you didn’t know to look for. Targeted metabolomics is built for precision: it measures a defined list of metabolites with high sensitivity and quantitative confidence. The challenge is that running both typically costs time, sample, and can introduce variability between workflows.
In order to deal with this the researchers at Thermo Fisher Scientific have developed Simultaneous Quantitation and Discovery (SQUAD) analysis as shown in this technical note Simultaneous Quantitation and Discovery Analysis: Combining Targeted and Untargeted Metabolomics on Orbitrap Mass Spectrometers, a hybrid strategy that combines targeted quantitation and untargeted discovery in a single experiment. In practice, SQUAD lets you quantify a predefined metabolite panel using calibration curves built from authentic standards and isotopically labeled internal standards, while still capturing rich full-scan data that supports retrospective mining and identification of unknowns.
A key theme of the technical note is that results are only as strong as the experiment design and quality controls. The workflow emphasizes calibration strategy, careful extraction choices (aligned to metabolite classes), and the smart use of blanks, pooled QCs, and system suitability tests to monitor drift, contamination, and reproducibility across a batch.
SQUAD is also designed to scale across different Thermo Scientific Orbitrap mass spectrometers. The technical note outlines how the Thermo Scientific Orbitrap Exploris mass spectrometers can use MS1-based SQUAD with polarity switching and optionally add tSIM/tMS2 for targeted sensitivity, while the Thermo Scientific Orbitrap Tribrid mass spectrometers can pair high-resolution MS1 discovery with rapid ion-trap tMS2 quantitation, boosted by tools like Thermo Scientific AcquireX Intelligent Data Acquisition and Real-Time Library Search (RTLS).
Finally, the data story comes together in software: Thermo Scientific TraceFinder Software for targeted quantitation and Thermo Scientific Compound Discoverer Software for untargeted discovery, annotation, and statistics, turning one injection into both confident numbers and new biological leads.
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